• Journal of Microbiology and Biotechnology
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• v.22 no.5
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• pp.600-606
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• 2012

Studies into the cell death program termed apoptosis have resulted in new information regarding how cells control and execute their own demise, including insights into the mechanism by which death-preventing factors can inhibit Bax-induced caspase activation. We investigated high temperature stress-induced cell death in Brassica rapa. Using a yeast functional screening from a Brassica rapa cDNA library, the BH5-127 EST clone encoding an apoptotic suppressor peptide was identified. However, a phylogenic tree showed that BH5-127 clusters within a clade containing SUMO-1 (Small Ubiquitin-like Modifier-1). BH5-127 was confirmed similar to have function to SUMO-1 as Fas suppression. Expression of BH5-127 showed that substantial suppression of cell death survived on SD-galactose-$Leu^-$-$Ura^-$ medium. The results suggest that BrSE ($\underline{B}$rassica rapa $\underline{S}$entrin $\underline{E}$ST, BH5-127) is one of the important regulatory proteins in programming cell death, especially in the seedling stage of Chinese cabbage.

• Journal of Species Research
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• v.8 no.3
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• pp.313-317
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• 2019

Bats influence overall ecosystem health by regulating species diversity and being a major source of zoonotic viruses. Hence, there is a need to elucidate their migration, population structure, and phylogenetic relationship. The complete mitochondrial genome is widely used for studying the genome-level characteristics and phylogenetic relationship of various animals due to its high mutation rate, simple structure, and maternal inheritance. In this study, we determined the complete mitogenome sequence of the bird-like noctule (Nyctalus aviator) by Illumina next-generation sequencing. The sequences obtained were used to reconstruct a phylogenic tree of Vespertilionidae to elucidate the phylogenetic relationship among its members. The mitogenome of N. aviator is 16,863-bp long with a typical vertebrate gene arrangement, consisting of 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 putative control region. Overall, the nucleotide composition is as follows: 32.3% A, 24.2% C, 14.3% G, and 29.2% T, with a slight AT bias (61.5%). The base composition of the 13 PCGs is as follows: 30.3% A, 13.4% G, 31.0% T, and 25.2% C. The phylogenetic analysis, based on 13 concatenated PCG sequences, infers that N. aviator is closely related to N. noctula with a high bootstrap value (100%).

• Korean Journal of Medicinal Crop Science
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• v.18 no.4
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• pp.266-272
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• 2010

There is a considerable difference in morphological traits between Bokbunja cultivated in Korea (KCB) and Korea native Rubus coreanus, contrary to the conviction that the cultivated Bokbunja is the domestication of R. coreanus. To infer the phylogenetic relationship of KCB with other Rubus species, we compared the chloroplast DNA spacers of KCB with those of several Rubus species including black raspberry, R. occidentalis. The three chloroplast DNA spacers, atpB~rbcL, trnL~trnF, and trnT~trnL, were amplified using the specific primer pairs and converted to Single Strand Conformational Polymorphism (SSCP) markers. The SSCP makers of the chloroplast DNA spacers showed a considerable variation both within and among Rubus species. In the phylogenetic tree generated by the SSCP markers, KCB accessions were located in the same clade with R. occidentalis, but R. coreanus accessions in the different clade. Also, in the phylogenetic tree by the nucleotide sequences of the chloroplast DNA spacer trnL~trnF, KCB located in the same clade with R. occidentalis but not with R. coreanus. These results suggest that the three KCB accessions share higher similarity with R. occidentalis than with R. coreanus in the three chloroplast DNA spacers.

• Genomics & Informatics
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• v.9 no.4
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• pp.181-188
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• 2011

In planning a model-based phylogenic study for highly related ethnic data, the SNP marker number is an important factor to determine for relationship inferences. Genotype frequency data, utilizing a sub sampling method, from 63 Pan Asian ethnic groups was used for determining the minimum SNP number required to establish such relationships. Bootstrap random sub-samplings were done from 5.6K PASNPi SNP data. DA distance was calculated and neighbour-joining trees were drawn with every re-sampling data set. Consensus trees were made with the same 100 sub-samples and bootstrap proportions were calculated. The tree consistency to the one obtained from the whole marker set, improved with increasing marker numbers. The bootstrap proportions became reliable when more than 7,000 SNPs were used at a time. Within highly related ethnic groups, the minimum SNPs number for a robust neighbor-joining tree inference was about 7,000 for a 95% bootstrap support.

• Journal of Life Science
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• v.22 no.3
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• pp.293-297
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• 2012

The movement of vesicles from the neuronal cell body to specific destinations requires molecular motors. The squid giant axon represents a powerful model for studies of the axonal transport mechanism because the axoplasm can readily be separated from the sheath by simple extrusion. In a previous study, vesicular movements in the axoplasm of the squid giant axon were inhibited by the kinesin antibody. In the present study, we cloned and sequenced the cDNAs for squid brain KIFs. Amplification of the conserved nucleotide sequences of the motor domain by polymerase chain reaction (PCR) using first-strand cDNAs of the squid optic lobe identified six new KIF proteins. Motif analysis of the motor domains revealed that the squid KIFs are homologous to the consensus sequences of the mouse KIFs. The phylogenetic tree generated by using the maximum parsimony (MP) method, the neighbor-joining (NJ) method, the minimum evolution (ME) method, and the maximum likelihood (ML) method showed that squid KIFs are closest to mouse KIFs. These data prove the phylogenetic relationships between squid KIFs and mouse ones.

• Microbiology and Biotechnology Letters
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• v.43 no.4
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• pp.307-313
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• 2015

Unpolished rice (UR) is considered to be a healthy alternative to white rice when coping with chronic diseases. In the present study, the fermented slurry of unpolished rice (FSUR) was evaluated with respect to its antimicrobial activities and biochemical characteristics, including the quantities of sugar, total soluble sugar, organic acids, free amino acids, pH, and physiological activity. The antimicrobial efficiency of FSUR was assessed using the paper disc-agar diffusion method. FSUR exhibited strong antimicrobial activity against six pathogenic bacterial strains (Staphylococcus aureus, Escherichia coli, Listeria monocytogenes, Pseudomonas aeruginosa, Salmonella typhimurium, and Yersinia enterocolitica) and two fermentation strains (Gluconacetobacter intermedius and Lodderomyces elongisporus). The antimicrobial activity of FSUR was higher than the commercial antibiotics, carbenicillin ($50{\mu}g/ml$) and tetracycline ($50{\mu}g/ml$) against S. aureus, E. coli, L. monocytogenes, P. aeruginosa, S. typhimurium, Y. enterocolitica, and L. elongisporus. Also FSUR had a high antioxidant activity. The microorganisms were isolated from FSUR using tryptic soy broth and yeast extract-peptone-dextrose agar media. The isolated microorganisms were characterized using physiological and biochemical analyses as well as by 16S rRNA gene sequencing and phylogenic analysis. 16S rRNA gene sequence analysis showed that the isolated microorganisms had a high similarity to G. intermedius, Lactobacillus casei, Lactobacillus plantarum, and Acetobacter peroxydans.

• Parasites, Hosts and Diseases
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• v.56 no.5
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• pp.515-519
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• 2018

Triatoma rubrofasciata is a wide-spread vector of Chagas disease in Americas. In this study, we completed the mitochondrial genome sequencing of T. rubrofasciata. The total length of T. rubrofasciata mitochondrial genome was 17,150 bp with the base composition of 40.4% A, 11.6% G, 29.4% T and 18.6% C. It included 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region. We constructed a phylogenetic tree on the 13 protein-coding genes of T. rubrofasciata and other 13 closely related species to show their phylogenic relationship. The determination of T. rubrofasciata mitogenome would play an important role in understanding the genetic diversity and evolution of triatomine bugs.

• Microbiology and Biotechnology Letters
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• v.31 no.2
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• pp.124-128
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• 2003

In order to isolate and characterize a novel fungal strain capable of producing cellulase, each samples of the old rice straw, soil, and the old tree were screened by congo red test. One of the fungi screened has been identified as Aspergillus tubingensis strain from the results of the phylogenic analysis based on partial DNA sequence and the basis of its biochemical properties. A carboxymethyl cellulase activity of the strain was higher than that of A. oryzae KCTC 6291. In CMCase activity measurement, it wasn't sensitive about pH 2.0, 3.0, 4.0, but the enzyme was more stable than A. oryzae under the various pH and temperature conditions and the enzyme activity was more similar to neutrality and alkali. Therefore, it could be suggested that the isolated strain has a potential possibility for the developing of the probiotics.

• Weed & Turfgrass Science
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• v.7 no.1
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• pp.22-34
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• 2018

Miscanthus has been considered as the most promising bioenergy crop for lignocellulosic biomass production. In Korea, M. sacchariflorus and M. sinensis can be found easily in all regions. It is a great advantage to utilize as important species with respect to genetic and cross-breeding programs materials for creation of novel hybrids. For successful breeding programs, it is important to precisely understand the variability of morphological and growth characteristics among Miscanthus species as breeding parent materials. In this study, morphological and growth characteristics were observed in 960 germplasms of two Miscanthus species (M. sacchariflorus and M. sinensis) for growing seasons over three years. Due to the inherent characteristics of these species, the germplasm of M. sacchariflorus among the collected germplasm were reduced in plant height than in the collection area. In M. sinensis, the plant height of germplasm collected mainly from Jeju-do increased more than those collected from collection area. Sixty-one of the collected 960 germplasms were selected and investigated to the morphological characteristics. Based on the investigated morphological data, the phylogenic tree was developed. As the results, it was confirmed that there exist germplasm in which the characteristics of M. sacchariflorus and M. sinensis are mixed. This study of Miscanthus may provide an important information in order to expedite the introduction as breeding materials for creation of new hybrid.

• Parasites, Hosts and Diseases
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• v.53 no.6
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• pp.719-724
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• 2015

Nematomorpha, horsehair or Gordian worms, include about 300 freshwater species in 22 genera (Gordiida) and 5 marine species in 1 marine genus (Nectonema). They are parasitic in arthropods during their juvenile stage. In the present study, the used gordian worm was found in the feces of a dog (5-month old, male) in July 2014. Following the worm analysis using light and scanning electron microscopes, the morphological classification was re-evaluated with molecular analysis. The worm was determined to be a male worm having a bi-lobed tail and had male gonads in cross sections. It was identified as Gordius sp. (Nematomorpha: Gordiidae) based on the characteristic morphologies of cross sections and areole on the cuticle. DNA analysis on 18S rRNA partial sequence arrangements was also carried out, and the gordiid worm was assumed to be close to the genus Gordius based on a phylogenic tree analysis.